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NM_016038.4(SBDS):c.258+2T>C AND not provided

Germline classification:
Pathogenic/Likely pathogenic (12 submissions)
Last evaluated:
Jul 23, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000255013.52

Allele description [Variation Report for NM_016038.4(SBDS):c.258+2T>C]

NM_016038.4(SBDS):c.258+2T>C

Gene:
SBDS:SBDS ribosome maturation factor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q11.21
Genomic location:
Preferred name:
NM_016038.4(SBDS):c.258+2T>C
Other names:
c.258+2T>C
HGVS:
  • NC_000007.14:g.66994210A>G
  • NG_007277.1:g.6392T>C
  • NG_033069.1:g.2406A>G
  • NM_016038.4:c.258+2T>CMANE SELECT
  • LRG_104t1:c.258+2T>C
  • LRG_104:g.6392T>C
  • NC_000007.13:g.66459197A>G
  • NM_016038.2:c.258+2T>C
  • NM_016038.2:c.[258+2T>C]
  • NM_016038.3:c.258+2T>C
Nucleotide change:
IVS2DS, T-C, +2
Links:
OMIM: 607444.0002; dbSNP: rs113993993
NCBI 1000 Genomes Browser:
rs113993993
Molecular consequence:
  • NM_016038.4:c.258+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
Functional consequence:
effect on RNA splicing [Variation Ontology: 0362]
Observations:
14

Condition(s)

Synonyms:
none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000321934GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Pathogenic
(Jan 2, 2020)
germlineclinical testing

Citation Link,

SCV000854947Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL ClinVar v180209 classification definitions)
Pathogenic
(Feb 26, 2018)
germlineclinical testing

Citation Link,

SCV000928088Blueprint Genetics
criteria provided, single submitter

(Blueprint Genetics Variant Classification Scheme)
Pathogenic
(Nov 30, 2018)
germlineclinical testing

Citation Link,

SCV001446830Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 23, 2020)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001501393CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Pathogenic
(Mar 1, 2024)
germlineclinical testing

Citation Link,

SCV001714209Mayo Clinic Laboratories, Mayo Clinic
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jul 23, 2024)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001743928Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus
no assertion criteria provided
Pathogenicgermlineclinical testing

SCV001797974Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus
no assertion criteria provided
Pathogenicgermlineclinical testing

SCV001808522Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus
no assertion criteria provided
Pathogenicgermlineclinical testing

SCV001958408Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Pathogenicgermlineclinical testing

SCV002011618Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Nov 3, 2021)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV005198124Clinical Genetics Laboratory, Skane University Hospital Lund
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jul 13, 2022)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes11not providednot provided1not providedclinical testing
not providedgermlineunknown3not providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From GeneDx, SCV000321934.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Canonical splice site variant in a gene for which loss-of-function is a known mechanism of disease; Results from a conversion event with a nearby SBDS pseudogene, an inactive gene with numerous pathogenic variants (Boocock et al., 2003); Published functional studies demonstrate that truncating variants, including c.258+2 T>C, may affect the protein's cellular localization and motility (Austin et al., 2005; Orelio et al., 2011); This variant is associated with the following publications: (PMID: 27127007, 15942154, 29620724, 16007594, 30109123, 12496757, 15860664, 21695142, 22934832, 14749921, 19148133, 22935661, 24629175, 25525159, 24426364, 26762974, 26866830, 17376717, 27153395, 26822237, 27431290, 17478638, 26492932, 15342903, 27519942, 25844324, 27290639, 15701631, 29716638, 25729736, 29146883, 23125299, 28102861, 28485484, 29375851, 30664904, 15474150, 30198570, 17920346, 30308536, 30105119, 27617157, 31321910, 31732620, 30894704, 32098966, 31965297, 32434641, 31019026, 32293785, 31980526, 32552793, 32581362, 32412173, 31589614, 32868804, 32888943)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Eurofins Ntd Llc (ga), SCV000854947.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided3not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided3not providednot providednot provided

From Blueprint Genetics, SCV000928088.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, SCV001446830.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot providednot providednot providednot providednot provided

From CeGaT Center for Human Genetics Tuebingen, SCV001501393.24

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided11not providednot providedclinical testingnot provided

Description

SBDS: PVS1, PS4:Moderate

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided11not providednot providednot provided

From Mayo Clinic Laboratories, Mayo Clinic, SCV001714209.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

PM1, PM3, PS3, PS4, PVS1

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001743928.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus, SCV001797974.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus, SCV001808522.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001958408.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden, SCV002011618.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Clinical Genetics Laboratory, Skane University Hospital Lund, SCV005198124.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jan 26, 2025